Thank you very much for uploading that. Connecting to that with the 1fb70... Windows executable compiled by Ves produces a near instant desync, so the problem does not appear to be of recent origin at all.
The next step is painstakingly to work out which features of the saved game cause the desync by testing either with certain features disabled in the code, or with saved games with those features not used. The latter may be a good place to start, as we have two very similar saved games, one which does and one which does not cause a desync.
Vladki - I wonder whether you could start by sending all the trains to the depot (you will be able to connect with Linux), and let me know when you have done that so that I can attempt to connect again.
Can anyone remember whether the game in the state in which it now exists has ever been playable on the server without desyncs when connected from a Windows client?
For reference, the date of this saved game was originally the 18th of September, and is the saved game that was uploaded to demonstrate the problems with trains apparently teleporting, which was since fixed.
Thank you both very much for your help so far.
Edit: One thought occurs to me - does anyone have a Windows executable from the last month or two built with Visual Studio 2012? It would be worthwhile trying that with a matching server version to see whether that makes any difference.